CRISPR Journal最新文献_第8页

Advances in Cas12a-Based Amplification-Free Nucleic Acid Detection. 基于Cas12a的扩增游离核酸检测研究进展。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2023-10-01 Epub Date: 2023-09-25 DOI: 10.1089/crispr.2023.0023

Shixin Ji, Xueli Wang, Yangkun Wang, Yingqi Sun, Yingying Su, Xiaosong Lv, Xiangwei Song

{"title":"Advances in Cas12a-Based Amplification-Free Nucleic Acid Detection.","authors":"Shixin Ji, Xueli Wang, Yangkun Wang, Yingqi Sun, Yingying Su, Xiaosong Lv, Xiangwei Song","doi":"10.1089/crispr.2023.0023","DOIUrl":"10.1089/crispr.2023.0023","url":null,"abstract":"In biomedicine, rapid and sensitive nucleic acid detection technology plays an important role in the early detection of infectious diseases. However, most traditional nucleic acid detection methods require the amplification of nucleic acids, resulting in problems such as long detection time, complex operation, and false-positive results. In recent years, clustered regularly interspaced short palindromic repeats (CRISPR) systems have been widely used in nucleic acid detection, especially the CRISPR-Cas12a system, which can trans cleave single-stranded DNA and can realize the detection of DNA targets. But, amplification of nucleic acids is still required to further improve detection sensitivity, which makes Cas12a-based amplification-free nucleic acid detection methods a great challenge. This article reviews the recent progress of Cas12a-based amplification-free detection methods for nucleic acids. These detection methods apply electrochemical detection methods, fluorescence detection methods, noble metal nanomaterial detection methods, and lateral flow assay. Under various optimization strategies, unamplified nucleic acids have the same sensitivity as amplified nucleic acids. At the same time, the article discusses the advantages and disadvantages of each method and further discusses the current challenges such as off-target effects and the ability to achieve high-throughput detection. Amplification-free nucleic acid detection technology based on CRISPR-Cas12a has great potential in the biomedical field.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":" ","pages":"405-418"},"PeriodicalIF":3.7,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41140397","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Measuring the Impact of Genetic Heterogeneity and Chromosomal Inversions on the Efficacy of CRISPR-Cas9 Gene Drives in Different Strains of Anopheles gambiae. 测量遗传异质性和染色体反转对CRISPR-Cas9基因驱动在不同冈比亚按蚊菌株中的效力的影响。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2023-10-01 Epub Date: 2023-09-13 DOI: 10.1089/crispr.2023.0029

Poppy Pescod, Giulia Bevivino, Amalia Anthousi, Ruth Shelton, Josephine Shepherd, Fabrizio Lombardo, Tony Nolan

{"title":"Measuring the Impact of Genetic Heterogeneity and Chromosomal Inversions on the Efficacy of CRISPR-Cas9 Gene Drives in Different Strains of Anopheles gambiae.","authors":"Poppy Pescod, Giulia Bevivino, Amalia Anthousi, Ruth Shelton, Josephine Shepherd, Fabrizio Lombardo, Tony Nolan","doi":"10.1089/crispr.2023.0029","DOIUrl":"10.1089/crispr.2023.0029","url":null,"abstract":"The human malaria vector Anopheles gambiae is becoming increasingly resistant to insecticides, spurring the development of genetic control strategies. CRISPR-Cas9 gene drives can modify a population by creating double-stranded breaks at highly specific targets, triggering copying of the gene drive into the cut site (\"homing\"), ensuring its inheritance. The DNA repair mechanism responsible requires homology between the donor and recipient chromosomes, presenting challenges for the invasion of laboratory-developed gene drives into wild populations of target species An. gambiae species complex, which show high levels of genome variation. Two gene drives (vas2-5958 and zpg-7280) were introduced into three An. gambiae strains collected across Africa with 5.3-6.6% variation around the target sites, and the effect of this variation on homing was measured. Gene drive homing across different karyotypes of the 2La chromosomal inversion was also assessed. No decrease in gene drive homing was seen despite target site heterology, demonstrating the applicability of gene drives to wild populations.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":" ","pages":"419-429"},"PeriodicalIF":3.7,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10215382","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genotyping MUltiplexed-Sequencing of CRISPR-Localized Editing (GMUSCLE): An Experimental and Computational Approach for Analyzing CRISPR-Edited Cells. CRISPR定位编辑的基因分型多重测序（GMUSCLE）：一种分析CRISPR编辑细胞的实验和计算方法。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2023-10-01 DOI: 10.1089/crispr.2023.0021

Peng Zhang, Laurent Abel, Jean-Laurent Casanova, Rui Yang

{"title":"Genotyping MUltiplexed-Sequencing of CRISPR-Localized Editing (GMUSCLE): An Experimental and Computational Approach for Analyzing CRISPR-Edited Cells.","authors":"Peng Zhang, Laurent Abel, Jean-Laurent Casanova, Rui Yang","doi":"10.1089/crispr.2023.0021","DOIUrl":"10.1089/crispr.2023.0021","url":null,"abstract":"Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) creates double-stranded breaks, the repair of which generates indels around the target sites. These repairs can be mono-/multi-allelic, and the editing is often random and sometimes prolonged, resulting in considerable intercellular heterogeneity. The genotyping of CRISPR-Cas9-edited cells is challenging and the traditional genotyping methods are laborious. We introduce here a streamlined experimental and computational protocol for genotyping CRISPR-Cas9 genome-edited cells including cost-effective multiplexed sequencing and the software Genotyping MUltiplexed-Sequencing of CRISPR-Localized Editing (GMUSCLE). In this approach, CRISPR-Cas9-edited products are sequenced in great depth, then GMUSCLE quantitatively and qualitatively identifies the genotypes, which enable the selection and investigation of cell clones with genotypes of interest. We validate the protocol and software by performing CRISPR-Cas9-mediated disruption on interferon-α/β receptor alpha, multiplexed sequencing, and identifying the genotypes simultaneously for 20 cell clones. Besides the multiplexed sequencing ability of this protocol, GMUSCLE is also applicable for the sequencing data from bulk cell populations. GMUSCLE is publicly available at our HGIDSOFT server and GitHub.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":"6 5","pages":"462-472"},"PeriodicalIF":3.7,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10611965/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41220060","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The CRISPR Toolbox: The End of the Beginning. CRISPR工具箱：开始的结束。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2023-10-01 DOI: 10.1089/crispr.2023.29167.editorial

Rodolphe Barrangou

引用次数: 0

Trichostatin A for Efficient CRISPR-Cas9 Gene Editing of Human Pluripotent Stem Cells. 曲霉菌素A用于人多能干细胞的有效CRISPR-Cas9基因编辑。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2023-10-01 Epub Date: 2023-09-07 DOI: 10.1089/crispr.2023.0033

Kaivalya Molugu, Namita Khajanchi, Cicera R Lazzarotto, Shengdar Q Tsai, Krishanu Saha

引用次数: 0

Pan-Coronavirus CRISPR-CasRx Effector System Significantly Reduces Viable Titer in HCoV-OC43, HCoV-229E, and SARS-CoV-2. 泛冠状病毒CRISPR-CasRx效应系统显著降低HCoV-OC43、HCoV-229E和SARS-CoV-2的活价

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2023-08-01 DOI: 10.1089/crispr.2022.0095

Cathryn M Mayes, Joshua L Santarpia

{"title":"Pan-Coronavirus CRISPR-CasRx Effector System Significantly Reduces Viable Titer in HCoV-OC43, HCoV-229E, and SARS-CoV-2.","authors":"Cathryn M Mayes, Joshua L Santarpia","doi":"10.1089/crispr.2022.0095","DOIUrl":"https://doi.org/10.1089/crispr.2022.0095","url":null,"abstract":"CRISPR-based technology has become widely used as an antiviral strategy, including as a broad-spectrum human coronavirus (HCoV) therapeutic. In this work, we have designed a CRISPR-CasRx effector system with guide RNAs (gRNAs) that are cross-reactive among several HCoV species. We tested the efficacy of this pan-coronavirus effector system by evaluating the reduction in viral viability associated with different CRISPR targets in HCoV-OC43, HCoV-229E, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We determined that several CRISPR targets significantly reduce viral titer, despite the presence of single nucleotide polymorphisms in the gRNA when compared with a non-targeting, negative control gRNA. CRISPR targets reduced viral titer between 85% and >99% in HCoV-OC43, between 78% and >99% in HCoV-229E, and between 70% and 94% in SARS-CoV-2 when compared with an untreated virus control. These data establish a proof-of-concept for a pan-coronavirus CRISPR effector system that is capable of reducing viable virus in both Risk Group 2 and Risk Group 3 HCoV pathogens.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":"6 4","pages":"359-368"},"PeriodicalIF":3.7,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10457650/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10152767","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

My CRISPR Story: Back to Brazil. 我的CRISPR故事:回到巴西。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2023-08-01 DOI: 10.1089/crispr.2023.0032

Daniel F M Monte

引用次数: 0

Discovery and Characterization of Novel Type V Cas12f Nucleases with Diverse Protospacer Adjacent Motif Preferences. 具有不同原间隔基序邻近基序偏好的新型V型Cas12f核酸酶的发现和表征

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2023-08-01 DOI: 10.1089/crispr.2023.0006

Allison Sharrar, Luisa Arake de Tacca, Trevor Collingwood, Zuriah Meacham, David Rabuka, Johanna Staples-Ager, Michael Schelle

{"title":"Discovery and Characterization of Novel Type V Cas12f Nucleases with Diverse Protospacer Adjacent Motif Preferences.","authors":"Allison Sharrar, Luisa Arake de Tacca, Trevor Collingwood, Zuriah Meacham, David Rabuka, Johanna Staples-Ager, Michael Schelle","doi":"10.1089/crispr.2023.0006","DOIUrl":"https://doi.org/10.1089/crispr.2023.0006","url":null,"abstract":"Small Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated (Cas) effectors are key to developing gene editing therapies due to the packaging constraints of viral vectors. While Cas9 and Cas12a CRISPR-Cas effectors have advanced into select clinical applications, their size is prohibitive for efficient delivery of both nuclease and guide RNA in a single viral vector. Type V Cas12f effectors present a solution given their small size. In this study, we describe a novel set of miniature (<490AA) Cas12f nucleases that cleave double-stranded DNA in human cells. We determined their optimal trans-activating RNA empirically through rational modifications, which resulted in an optimal single guide RNA. We show that these nucleases have broad protospacer adjacent motif (PAM) preferences, allowing for expanded genome targeting. The unique characteristics of these novel nucleases add to the diversity of the miniature CRISPR-Cas toolbox while the expanded PAM allows for the editing of genomic locations that could not be accessed with existing Cas12f nucleases.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":"6 4","pages":"350-358"},"PeriodicalIF":3.7,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10037354","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Predicting Mutations Generated by Cas9, Base Editing, and Prime Editing in Mammalian Cells. 预测哺乳动物细胞中Cas9、碱基编辑和引体编辑产生的突变。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2023-08-01 DOI: 10.1089/crispr.2023.0016

Juliane Weller, Ananth Pallaseni, Jonas Koeppel, Leopold Parts

引用次数: 0

Rosalind Franklin Society Proudly Announces the 2022 Award Recipient for The CRISPR Journal. 罗莎琳德·富兰克林协会自豪地宣布了2022年CRISPR杂志的获奖者。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2023-08-01 DOI: 10.1089/crispr.2023.29162.rfs2022

Nicole F Brackett

引用次数: 0